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Effective URL: https://www.gutcellatlas.org/
Submission: On February 01 via manual from IN — Scanned from GB
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* Datasets * Publications * Funders * Team * Collaborators by Teichlab Wellcome Sanger Institute Part of Human Cell Atlas DATASETS * chevron_rightSpace-Time Gut Cell Atlas Summary Interactive Viewer Norm H5AD Data Raw H5AD Data RNA Velocyto Full single cell RNA-seq dataset of 428K intestinal cells from fetal, pediatric, adult donors, and up to 11 intestinal regions. Click here to access the paper. pageview file_download file_download file_download Explore lineages below: Epithelium pageview file_download file_download Mesenchyme pageview file_download file_download Enteric neurons pageview file_download file_download Endothelium pageview file_download file_download T/NK cells pageview file_download file_download B cells pageview file_download file_download Myeloid pageview file_download file_download * chevron_rightFetal and Pediatric Cell Atlas Summary Interactive Viewer Norm H5AD Data Raw H5AD Data Single-cell transcriptomes for 62,849 cells isolated from 6-11 weeks post-conception developing human gut. This data includes intestinal cells from duo-jejunum, ileum and colon. pageview file_download file_download Single-cell transcriptomes isolated from terminal ileum of childhood onset Crohn’s disease and matched healthy controls. This map includes total of 22,500 cells from 8 control samples and 7 Chron’s disease samples. pageview file_download file_download Human fetal epithelium architecture before crypt-villus emergence. pageview Emergence of intestinal stem cells (green, LGR5) in the human fetal intestine. pageview Human enteric nervous system development. Colonisation of the myenteric plexus by enteric neural progenitors. pageview Gut immune system development. Surveilance by lymphoid tissue initiator (LTi) cells. pageview Histology & RNAscope imaging by the Cellular Generation and Phenotyping (CGaP) core facility and Bayraktar Lab. * chevron_rightColon Immune Atlas Summary Interactive Viewer H5AD Data MTX Counts CSV Gene Names CSV Metadata The colon, as a barrier tissue, represents a unique immune environment where immune cells display tolerance toward adiverse community of microbes, which are collectively known as the microbiome. The published study revealed that not only were there differences between the immune cells in different parts of the colon, but that the microbiome also subtly changed, with a broader range of bacteria further down the colon. Image Description: Single cell transcriptomes for 41,650 cells isolated from the caeacum, transverse colon and sigmoid colon of 5 individuals. Single cell transcriptomes for 41,650 cells isolated from the caeacum, transverse colon and sigmoid colon of 5 individuals. pageview file_download file_download file_download file_download PUBLICATIONS Cells of the human intestinal tract mapped across space and time. Rasa Elmentaite, Natsuhiko Kumasaka, Kenny Roberts, Aaron Fleming, Emma Dann, Hamish W. King, Vitalii Kleshchevnikov, Monika Dabrowska, Sophie Pritchard, Liam Bolt, Sara F. Vieira, Lira Mamanova, Ni Huang, Francesca Perrone, Issac Goh Kai’En, Steven N. Lisgo, Matilda Katan, Steven Leonard, Thomas R. W. Oliver, C. Elizabeth Hook, Komal Nayak, Lia S. Campos, Cecilia Domínguez Conde, Emily Stephenson, Justin Engelbert, Rachel A. Botting, Krzysztof Polanski, Stijn van Dongen, Minal Patel, Michael D. Morgan, John C. Marioni, Omer Ali Bayraktar, Kerstin B. Meyer, Xiaoling He, Roger A. Barker, Holm H. Uhlig, Krishnaa T. Mahbubani, Kourosh Saeb-Parsy, Matthias Zilbauer, Menna R. Clatworthy, Muzlifah Haniffa, Kylie R. James & Sarah A. Teichmann 2021 Sep 08 link Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease. Rasa Elmentaite, Alexander D.B.Ross, KennyRoberts, Kylie R.James, Daniel Ortmann, Tomás Gomes, Komal Nayak, Liz Tuck, Sophie Pritchard, Omer Ali Bayraktar, Robert Heuschkel, Ludovic Vallier, Sarah A.Teichmann, Matthias Zilbauer 2020 Dec 21 link Distinct microbial and immune niches of the human colon Kylie R. James, Tomas Gomes, Rasa Elmentaite, Nitin Kumar, Emily L. Gulliver, Hamish W. King, Mark D. Stares, Bethany R. Bareham, John R. Ferdinand, Velislava N. Petrova, Krzysztof Polański, Samuel C. Forster, Lorna B. Jarvis, Ondrej Suchanek, Sarah Howlett, Louisa K. James, Joanne L. Jones, Kerstin B. Meyer, Menna R. Clatworthy, Kourosh Saeb-Parsy, Trevor D. Lawley & Sarah A. Teichmann 2020 Feb 17 link FUNDERS TEAM Sarah Teichmann FMedSci FRS Wellcome Sanger Institute & University of Cambridge @Teichlab Matthias Zilbauer University Lecturer and Hon. Consultant Department of Paediatrics University of Cambridge Kylie James Group Leader Garvan Institute, Sydney @KylieReneeJames Rasa Elmentaite PhD candidate Wellcome Sanger Institute @elmentaite Alexander Ross MBBS PhD NIHR Academic Clinical Fellow and Honorary Specialty Registrar in Medical Genetics University of Cambridge COLLABORATING GROUPS Haniffa Group Clatworthy Group Uhlig Group Saeb-Parsy Group Barker Group Bayraktar Group Marioni Group This site is hosted by Wellcome Sanger Institute Cookies policy | Terms and Conditions